Evolution and spread of SARS-CoV-2 likely to be affected by climate

Bajaj, Priyanka; Arya, Prakash Chandra

doi:10.1016/j.ecochg.2021.100005

Cited by 7 publications

(5 citation statements)

References 37 publications

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“…Using molecular phylogenetic analysis, Bajaj and Arya [ 120 ] studied the SARS-CoV-2 evolution and its relationship to abiotic factors (humidity, precipitation, radiation, temperature, and wind speed). These studies pointed out two genetically distinct variant groups G1 and G2 on the basis of four mutations.…”

Section: Resultsmentioning

confidence: 99%

The effects of air pollution, meteorological parameters, and climate change on COVID-19 comorbidity and health disparities: A systematic review

Juárez

Ramesh

Hood

et al. 2022

Environmental Chemistry and Ecotoxicology

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Section: Resultsmentioning

confidence: 99%

The effects of air pollution, meteorological parameters, and climate change on COVID-19 comorbidity and health disparities: A systematic review

Juárez

Ramesh

Hood

et al. 2022

Environmental Chemistry and Ecotoxicology

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“…[7][8][9] While these methods are useful in providing atomic level information but are labor intensive and not easily parallelizable. The advent of next generation sequencing has revolutionized biology, 1,10 resulting in the development of various approaches that can be used to predict structural features in the absence of a structure. 2,11 Alanine scanning and cysteine scanning mutagenesis approaches have been previously used to predict functional residues but have limitations.…”

Section: Introductionmentioning

confidence: 99%

Structural and functional determinants inferred from deep mutational scans

2022

Self Cite

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Mutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analyzing mutant phenotypes in the CcdB-sensitive, CcdBresistant, and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterized to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.

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“…While these methods are useful in providing atomic level information but are labour intensive and not easily parallelizable. The advent of next generation sequencing has revolutionised biology 1, 10 , resulting in the development of various approaches that can be used to predict structural features in the absence of a structure 2, 11 . Alanine scanning, and cysteine scanning mutagenesis approaches have been previously used to predict functional residues but have limitations.…”

Section: Introductionmentioning

confidence: 99%

Structural and functional determinants inferred from deep mutational scans

Bajaj

Manjunath

Varadarajan

2022

Preprint

Self Cite

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Mutations that affect protein binding to a cognate partner primarily occur either at buried residues or at exposed residues directly involved in partner binding. Distinguishing between these two categories based solely on mutational phenotypes is challenging. The bacterial toxin CcdB kills cells by binding to DNA Gyrase. Cell death is prevented by binding to its cognate antitoxin CcdA, at an extended interface that partially overlaps with the GyrA binding site. Using the CcdAB toxin-antitoxin (TA) system as a model, a comprehensive site-saturation mutagenesis library of CcdB was generated in its native operonic context. The mutational sensitivity of each mutant was estimated by evaluating the relative abundance of each mutant in two strains, one resistant and the other sensitive to the toxic activity of the CcdB toxin, through deep sequencing. The ability to bind CcdA was inferred through a RelE reporter gene assay, since the CcdAB complex binds to its own promoter, repressing transcription. By analysing mutant phenotypes in the CcdB sensitive, CcdB resistant and RelE reporter strains, it was possible to assign residues to buried, CcdA interacting or GyrA interacting sites. A few mutants were individually constructed, expressed, and biophysically characterised to validate molecular mechanisms responsible for the observed phenotypes. Residues inferred to be important for antitoxin binding, are also likely to be important for rejuvenating CcdB from the CcdB-Gyrase complex. Therefore, even in the absence of structural information, when coupled to appropriate genetic screens, such high-throughput strategies can be deployed for predicting structural and functional determinants of proteins.

show abstract

Evolution and spread of SARS-CoV-2 likely to be affected by climate

Cited by 7 publications

References 37 publications

The effects of air pollution, meteorological parameters, and climate change on COVID-19 comorbidity and health disparities: A systematic review

The effects of air pollution, meteorological parameters, and climate change on COVID-19 comorbidity and health disparities: A systematic review

Structural and functional determinants inferred from deep mutational scans

Structural and functional determinants inferred from deep mutational scans

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